Diff of the two buildlogs: -- --- b1/build.log 2024-03-26 02:49:55.493566938 +0000 +++ b2/build.log 2024-03-26 02:55:09.632167332 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Mar 25 14:43:01 -12 2024 -I: pbuilder-time-stamp: 1711420981 +I: Current time: Mon Apr 28 23:13:06 +14 2025 +I: pbuilder-time-stamp: 1745831586 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -39,54 +39,86 @@ dpkg-source: info: applying skip_install_BEAST_package.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/17811/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/96593/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 28 09:13 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/96593/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/96593/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='27a519a07ec445f99a02ce9779f058ec' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='17811' - PS1='# ' - PS2='> ' + INVOCATION_ID=01d141f6597e417f87b398d45c0ab1b9 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=96593 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6loLilad/pbuilderrc_dbZv --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6loLilad/b1 --logfile b1/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6loLilad/pbuilderrc_Ue06 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6loLilad/b2 --logfile b2/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 25 11:27 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/17811/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 25 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/96593/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -466,7 +498,7 @@ Get: 314 http://deb.debian.org/debian trixie/main i386 libjam-java all 0.1.git20180106.740247a+dfsg-1 [164 kB] Get: 315 http://deb.debian.org/debian trixie/main i386 libopenjfx-jni i386 11.0.11+1-3.1 [20.3 MB] Get: 316 http://deb.debian.org/debian trixie/main i386 libopenjfx-java all 11.0.11+1-3.1 [8903 kB] -Fetched 366 MB in 8s (45.5 MB/s) +Fetched 366 MB in 4s (82.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19816 files and directories currently installed.) @@ -1510,8 +1542,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Mar 26 02:44:18 UTC 2024. -Universal Time is now: Tue Mar 26 02:44:18 UTC 2024. +Local time is now: Mon Apr 28 09:13:52 UTC 2025. +Universal Time is now: Mon Apr 28 09:13:52 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libdconf1:i386 (0.40.0-4+b1) ... @@ -1964,7 +1996,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../beast2-mcmc_2.7.6+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/96593/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/96593/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../beast2-mcmc_2.7.6+dfsg-1_source.changes dpkg-buildpackage: info: source package beast2-mcmc dpkg-buildpackage: info: source version 2.7.6+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2083,7 +2119,7 @@ [jar] Building jar: /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/dist/BEAST.app.jar BUILD SUCCESSFUL -Total time: 39 seconds +Total time: 25 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' @@ -2117,6 +2153,12 @@ [java] 768 sites [java] 69 patterns [java] + [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", + [java] p: [ + [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [1.0, 3.0] }, + [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [3.0, 4.0] } + [java] ] + [java] } [java] OK [java] test getCitation [java] test initByName @@ -2125,19 +2167,13 @@ [java] test getInputValue [java] test getOutputs [java] Validation error when initializing object test.beast.core.BEASTInterfaceTest$BEASTi (id null): - [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", - [java] p: [ - [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [1.0, 3.0] }, - [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [3.0, 4.0] } - [java] ] - [java] } - [java] Failed to set the string value to '1e-1' for beastobject id=nullWriting file beast.log + [java] Failed to set the string value to '1e-1' for beastobject id=null [java] Failed to set the string value to '21474836470' for beastobject id=null - [java] WARNING: Operator scaleOperator.Species is contained in multiple operator schedules. - [java] Operator weighting may not work as expected. - [java] + [java] Writing file beast.log [java] Sample null.1 null.2 [java] 1 0.3 0.7 -- + [java] WARNING: Operator scaleOperator.Species is contained in multiple operator schedules. + [java] Operator weighting may not work as expected. [java] seq1: 3 4 [java] seq2: 3 4 [java] seq3: 3 4 @@ -2190,7 +2226,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.254 seconds + [java] Total calculation time: 1.635 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516753 variance: 1.7216547315139537 ESS: 25717.88066361133 @@ -2222,13 +2258,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.369 seconds + [java] Total calculation time: 2.035 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326598056 variance: 0.00998468201961599 ESS: 199303.5697419037 [java] ------------------------------------------------- [java] [java] trace log written to /tmp/bactrian.log + [java] End likelihood: 1.3580153849811107 [java] =============================================================================== [java] Citations for this model: [java] @@ -2242,7 +2279,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -0.6931471805599453 - [java] End likelihood: 1.3580153849811107 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianIntervalOperator(unknown) 3.89367 611282 1388719 1.00000 0.30564 @@ -2254,13 +2290,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.209 seconds + [java] Total calculation time: 1.745 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: -0.9999141170712321 variance: 0.33333524355318095 ESS: 198672.26933150744 [java] ------------------------------------------------- [java] [java] trace log written to /tmp/bactrian.log + [java] End likelihood: -0.6931471805599453 [java] =============================================================================== [java] Citations for this model: [java] @@ -2274,7 +2311,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -0.6931471805599453 - [java] End likelihood: -0.6931471805599453 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianIntervalOperator(unknown) 3.89367 611282 1388719 1.00000 0.30564 @@ -2286,12 +2322,13 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.2 seconds + [java] Total calculation time: 1.901 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.0000858829347083 variance: 0.3333352435532249 ESS: 198672.2693314681 [java] ------------------------------------------------- [java] + [java] End likelihood: -0.6931471805599453 [java] trace log written to /tmp/bactrian.log [java] =============================================================================== [java] Citations for this model: @@ -2306,7 +2343,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -0.6931471805599453 - [java] End likelihood: -0.6931471805599453 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianIntervalOperator(unknown) 3.89367 611282 1388719 1.00000 0.30564 @@ -2318,13 +2354,12 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.245 seconds + [java] Total calculation time: 1.889 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0000858834570785 variance: 0.3333352435537157 ESS: 198672.26933227608 [java] ------------------------------------------------- [java] - [java] End likelihood: -0.6931471805599453 [java] trace log written to /tmp/bactrian.log [java] Starting frequencies: [0.3333333, 0.3333333, 0.3333333] [java] freqs = @@ -2341,6 +2376,21 @@ [java] [java] transition prob : [java] [0.6674871505723157, 0.22927797953210746, 0.10323486989557647, 0.2292779795321076, 0.415400931299253, 0.35532108916863914, 0.10323486989557647, 0.3553210891686388, 0.5414440409357847] + [java] row 0 prob sum = 0.9999999999999996 + [java] row 1 prob sum = 0.9999999999999998 + [java] row 2 prob sum = 0.9999999999999999 + [java] End likelihood: -0.6931471805599453 + [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] + [java] Struthio_camelus: 85 20 + [java] Rhea_americana: 85 20 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2363,20 +2413,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic - [java] row 0 prob sum = 0.9999999999999996 - [java] row 1 prob sum = 0.9999999999999998 - [java] row 2 prob sum = 0.9999999999999999 - [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] - [java] Struthio_camelus: 85 20 - [java] Rhea_americana: 85 20 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] human: 772 4 [java] chimp: 772 4 [java] bonobo: 772 4 @@ -2391,37 +2427,6 @@ [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2460,33 +2465,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] 6.821210263296962E-13 - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2517,19 +2495,6 @@ [java] Starting frequencies: [1.0, 0.0] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] - [java] Struthio_camelus: 85 20 - [java] Rhea_americana: 85 20 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2537,16 +2502,11 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. + [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. + [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -2575,6 +2535,7 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic + [java] 6.821210263296962E-13 [java] Using ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. @@ -2586,21 +2547,25 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. + [java] With 50 unique site patterns. [java] Using rescaling scheme : dynamic [java] Using ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. + [java] With 50 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] + [java] Struthio_camelus: 85 20 + [java] Rhea_americana: 85 20 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -2770,12 +2735,8 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2783,12 +2744,8 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2796,12 +2753,8 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2809,12 +2762,8 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2822,12 +2771,12 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 6 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 6 unique site patterns. - [java] Using rescaling scheme : none + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2835,11 +2784,11 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 64 unique site patterns. + [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. + [java] Using ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 64 unique site patterns. + [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -2857,12 +2806,12 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] Using character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2870,12 +2819,25 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2883,12 +2845,25 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] With 6 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 6 unique site patterns. + [java] Using rescaling scheme : none [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2896,17 +2871,21 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. + [java] With 64 unique site patterns. [java] Using rescaling scheme : dynamic [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. + [java] With 64 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -3026,6 +3005,80 @@ [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] German_ST: 5051 4 + [java] Dutch_List: 5051 4 + [java] English_ST: 5051 4 + [java] French: 5051 4 + [java] Italian: 5051 4 + [java] Spanish: 5051 4 + [java] Stripping invariant sites + [java] <0> <1> removed 4486 sites + [java] Alignment(null) + [java] 6 taxa + [java] 5051 sites with weight 565 + [java] 50 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. @@ -3087,23 +3140,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [java] German_ST: 5051 4 - [java] Dutch_List: 5051 4 - [java] English_ST: 5051 4 - [java] French: 5051 4 - [java] Italian: 5051 4 - [java] Spanish: 5051 4 - [java] Stripping invariant sites - [java] <0> <1> removed 4486 sites - [java] Alignment(null) - [java] 6 taxa - [java] 5051 sites with weight 565 - [java] 50 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Starting frequencies: [0.07207207207207206, 0.006006006006006005, 0.019019019019019014, 0.02402402402402402, 0.061061061061061045, 0.05605605605605604, 0.02802802802802802, 0.08808808808808806, 0.023023023023023018, 0.16816816816816815, 0.05405405405405404, 0.039039039039039033, 0.05405405405405404, 0.02502502502502502, 0.019019019019019014, 0.07207207207207206, 0.08608608608608606, 0.04304304304304303, 0.029029029029029024, 0.033033033033033024] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -3208,6 +3244,19 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] =============================================================================== + [java] Citations for this model: + [java] + [java] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, + [java] Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, + [java] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, + [java] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, + [java] Alexei J. Drummond + [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. + [java] PLoS computational biology 15, no. 4 (2019): e1006650. + [java] + [java] =============================================================================== + [java] Start likelihood: -14.297530455869882 [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3378,19 +3427,6 @@ [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [java] =============================================================================== - [java] Citations for this model: - [java] - [java] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, - [java] Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, - [java] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, - [java] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, - [java] Alexei J. Drummond - [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - [java] PLoS computational biology 15, no. 4 (2019): e1006650. - [java] - [java] =============================================================================== - [java] Start likelihood: -14.297530455869882 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.30772 308831 691170 1.00000 0.30883 @@ -3402,7 +3438,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.221 seconds + [java] Total calculation time: 2.165 seconds [java] End likelihood: -2.1015817812114337 [java] =============================================================================== [java] Citations for this model: @@ -3417,7 +3453,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -7.148765227934941 - [java] End likelihood: 0.008929267909651761 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.31053 307447 692554 1.00000 0.30745 @@ -3429,7 +3464,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.735 seconds + [java] Total calculation time: 1.658 seconds + [java] End likelihood: 0.008929267909651761 [java] =============================================================================== [java] Citations for this model: [java] @@ -3455,7 +3491,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.283 seconds + [java] Total calculation time: 2.212 seconds [java] End likelihood: -0.5552616722750887 [java] =============================================================================== [java] Citations for this model: @@ -3470,6 +3506,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 + [java] End likelihood: -2.422052674650429 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.23542 303560 696441 1.00000 0.30356 @@ -3481,8 +3518,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.49 seconds - [java] End likelihood: -2.422052674650429 + [java] Total calculation time: 3.227 seconds [java] A: 1 4 [java] B: 1 4 [java] C: 1 4 @@ -3540,7 +3576,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.39 seconds + [java] Total calculation time: 1.072 seconds [java] End likelihood: 3.1192013590196357 [java] Testing mirror distribution [java] Testing mirror distribution for scaling @@ -3570,6 +3606,17 @@ [java] Testing bactrian_triangle s= 0.999423750532334 [java] Testing bactrian_triangle s= 0.9998030418762279 [java] Testing bactrian_box s= 0.9993617332307378 + [java] Testing bactrian_box s= 0.9993638943013682 + [java] Number of weights (4) does not match sequence length (16) + [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] + [java] 0human AAAACCCCGGGGTTTT + [java] 1chimp ACGTACGTACGTACGT + [java] [11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] + [java] AAAACCCCTTTTGGGG + [java] ACTGACGTACGTACGT + [java] [101000, 10000, 1, 110] + [java] GGGAAA + [java] AGGACA [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) @@ -3823,17 +3870,6 @@ [java] [java] t0 = 0 (0.0) [java] t1 = 10 (10.0) - [java] Testing bactrian_box s= 0.9993638943013682 - [java] Number of weights (4) does not match sequence length (16) - [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] - [java] 0human AAAACCCCGGGGTTTT - [java] 1chimp ACGTACGTACGTACGT - [java] [11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] - [java] AAAACCCCTTTTGGGG - [java] ACTGACGTACGTACGT - [java] [101000, 10000, 1, 110] - [java] GGGAAA - [java] AGGACA [java] java.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. [java] at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) @@ -4087,7 +4123,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.609 seconds + [java] Total calculation time: 2.538 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.9998844142873339 variance: 0.9962228119352623 ESS: 194315.96975230493 @@ -4119,7 +4155,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 5.694 seconds + [java] Total calculation time: 3.113 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516753 variance: 1.7216547315139537 ESS: 25717.88066361133 @@ -4127,6 +4163,22 @@ [java] [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.8084620917494391 + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] + [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] Expected: [0.1584087537031632, 0.01389998976971136, 0.7609221549346824, 0.06676910159244315] + [java] Calculat: [0.15840875370312343, 0.013899989769708488, 0.7609221549344917, 0.06676910159242638, 0.1584087537031232, 0.013899989769708469, 0.7609221549344906, 0.0667691015924263, 0.15840875370312313, 0.01389998976970846, 0.7609221549344901, 0.06676910159242626, 0.15840875370312307, 0.013899989769708455, 0.7609221549344899, 0.06676910159242623] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] @@ -4162,22 +4214,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -6.753673320834167 - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] - [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Expected: [0.1584087537031632, 0.01389998976971136, 0.7609221549346824, 0.06676910159244315] - [java] Calculat: [0.15840875370312343, 0.013899989769708488, 0.7609221549344917, 0.06676910159242638, 0.1584087537031232, 0.013899989769708469, 0.7609221549344906, 0.0667691015924263, 0.15840875370312313, 0.01389998976970846, 0.7609221549344901, 0.06676910159242626, 0.15840875370312307, 0.013899989769708455, 0.7609221549344899, 0.06676910159242623] [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianUpDownOperator(unknown) 0.02500 435934 2062466 0.50000 0.17449 @@ -4191,7 +4227,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 16.783 seconds + [java] Total calculation time: 11.048 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.999687438964741 variance: 1.681551176507236 ESS: 106131.39271214437 @@ -4209,10 +4245,6 @@ [java] 32 patterns [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] [java] human: 772 4 [java] chimp: 772 4 @@ -4280,6 +4312,11 @@ [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] 1.1368683772161603E-12 [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [java] German_ST: 5051 2 @@ -4353,7 +4390,6 @@ [java] 768 sites [java] 69 patterns [java] - [java] 1.1368683772161603E-12 [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 @@ -4690,16 +4726,6 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] - [java] t 0=0 - [java] t 1=1 - [java] t 2=2 - [java] t 3=3 - [java] t 4=4 - [java] t 5=5 - [java] t 6=6 - [java] t 7=7 - [java] t 8=8 - [java] t 9=9 [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -4752,6 +4778,16 @@ [java] t 7 = 7 (7.0) [java] t 8 = 8 (8.0) [java] t 9 = 9 (9.0) + [java] t 0=0 + [java] t 1=1 + [java] t 2=2 + [java] t 3=3 + [java] t 4=4 + [java] t 5=5 + [java] t 6=6 + [java] t 7=7 + [java] t 8=8 + [java] t 9=9 [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -15033,12 +15069,6 @@ [java] at java.base/java.lang.Double.(Double.java:733) [java] ... 111 more [java] adfgad - [java] exception thrown - [java] /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) - [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus - [java] exception thrown - [java] Cannot read the array length because "" is null - [java] (C:10.0,(B:20.0,A:30.0):10.0):0.0 [java] java.lang.reflect.InvocationTargetException [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) @@ -15386,6 +15416,16 @@ [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [java] exception thrown + [java] /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) + [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus + [java] exception thrown + [java] Cannot read the array length because "" is null + [java] (C:10.0,(B:20.0,A:30.0):10.0):0.0 + [java] + [java] WARNING: Delegated to the 'execute' command. + [java] This behaviour has been deprecated and will be removed in a future release. + [java] Please use the 'execute' command directly. [java] ╷ [java] ├─ JUnit Platform Suite ✔ [java] ├─ JUnit Jupiter ✔ @@ -15400,9 +15440,6 @@ [java] │ │ ├─ testGetKey() ✔ [java] │ │ ├─ testParamter() ✔ [java] │ │ └─ testKeysTwoColumns() ✔ - [java] │ ├─ BEASTInterfaceTest ✔ - [java] │ │ ├─ testInputType() ✔ - [java] │ │ └─ testBEASTi() ✔ [java] │ ├─ InputForAnnotatedConstructorTest ✔ [java] │ │ ├─ testEnumerationInput() ✔ [java] │ │ ├─ testArrayInput() ✔ @@ -15413,19 +15450,24 @@ [java] │ │ ├─ testJSON() ✔ [java] │ │ ├─ testInnerClass() ✔ [java] │ │ └─ testPrimitiveInput() ✔ + [java] │ ├─ BEASTInterfaceTest ✔ + [java] │ │ ├─ testInputType() ✔ + [java] │ │ └─ testBEASTi() ✔ [java] │ ├─ LoggerTest ✔ [java] │ │ ├─ testFileLog() ✔ [java] │ │ ├─ testScreenLog() ✔ [java] │ │ └─ isLoggingToStdout() ✔ - [java] │ ├─ BooleanParameterListTest ✔ - [java] │ │ └─ test1() ✔ [java] │ ├─ InputTest ✔ [java] │ │ ├─ testOptionalInput() ✔ [java] │ │ ├─ testScientificNotationDecimalFailure() ✔ [java] │ │ ├─ testScienticNotation() ✔ [java] │ │ └─ testScientificNotationIntTooLarge() ✔ + [java] │ ├─ BooleanParameterListTest ✔ + [java] │ │ └─ test1() ✔ [java] │ ├─ IntegerParameterListTest ✔ [java] │ │ └─ test1() ✔ + [java] │ ├─ SumTest ✔ + [java] │ │ └─ testSum() ✔ [java] │ ├─ OperatorScheduleTest ✔ [java] │ │ ├─ testOperatorScheduleMultiNestedByPercentageAndRelativeWeight() ✔ [java] │ │ ├─ testOperatorScheduleNestedByPercentage() ✔ @@ -15435,12 +15477,6 @@ [java] │ │ ├─ testOperatorScheduleNestedByRelativeWeight() ✔ [java] │ │ ├─ testOperatorSchedulePlain() ✔ [java] │ │ └─ testOperatorScheduleNestedByRelativeWeight2() ✔ - [java] │ ├─ SumTest ✔ - [java] - [java] WARNING: Delegated to the 'execute' command. - [java] This behaviour has been deprecated and will be removed in a future release. - [java] Please use the 'execute' command directly. - [java] │ │ └─ testSum() ✔ [java] │ ├─ UncertainAlignmentTest ✔ [java] │ │ └─ testUncertainAlignment() ✔ [java] │ ├─ BactrianIntervalOperatorTest ✔ @@ -15501,19 +15537,19 @@ [java] │ │ ├─ testScaleAllIndependentlylDistribution() ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ ExchangeOperatorTest ✔ - [java] │ │ ├─ testNarrowExchange4Taxa() ✔ - [java] │ │ ├─ testNarrowExchange5Taxa() 10466 ms ✔ - [java] │ │ └─ testNarrowExchange6Taxa() 10110 ms ✔ + [java] │ │ ├─ testNarrowExchange4Taxa() 11574 ms ✔ + [java] │ │ ├─ testNarrowExchange5Taxa() ✔ + [java] │ │ └─ testNarrowExchange6Taxa() ✔ [java] │ ├─ BactrianDeltaExchangeOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ [java] │ │ ├─ testLogNormalDistribution() ✔ [java] │ │ ├─ testKeepsSum() ✔ [java] │ │ ├─ testCanOperate() ✔ [java] │ │ └─ testKeepsWeightedSum() ✔ - [java] │ ├─ ScaleOperatorTest ✔ - [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ YuleModelTest ✔ [java] │ │ └─ testYule() ✔ + [java] │ ├─ ScaleOperatorTest ✔ + [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ NodeTest ✔ [java] │ │ ├─ testToNewick() ✔ [java] │ │ ├─ testRootToString() ✔ @@ -15540,16 +15576,16 @@ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ IntRandomWalkOperatorTest ✔ [java] │ │ ├─ testIntRandomWalkDistribution3x6() ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x10() 16602 ms ✔ - [java] │ │ └─ testIntRandomWalkDistribution6x10() 25913 ms ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x10() 13859 ms ✔ + [java] │ │ └─ testIntRandomWalkDistribution6x10() 23770 ms ✔ [java] │ ├─ BactrianRandomWalkOperatorTest ✔ - [java] │ │ ├─ testNormalDistribution() 13161 ms ✔ - [java] │ │ └─ testLogNormalDistribution() 17830 ms ✔ + [java] │ │ ├─ testNormalDistribution() ✔ + [java] │ │ └─ testLogNormalDistribution() ✔ [java] │ ├─ BinaryCovarionModelTest ✔ [java] │ │ └─ testEquilibriumFrequencies() ✔ [java] │ ├─ BactrianUpDownOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ └─ testLogNormalDistribution() 36656 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 24741 ms ✔ [java] │ ├─ TreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -15593,7 +15629,7 @@ [java] │ ├─ CompoundParameterHelperTest ✔ [java] │ │ └─ testCompoundParameterHelper() ✔ [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 21573 ms ✔ + [java] │ │ └─ testCoalescentTimes() 19456 ms ✔ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ @@ -15652,7 +15688,7 @@ [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 245662 ms + [java] Test run finished after 198288 ms [java] [ 51 containers found ] [java] [ 0 containers skipped ] [java] [ 51 containers started ] @@ -15666,10 +15702,10 @@ [java] [ 207 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null1588913299 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null2073971014 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 1141ms -[junitreport] Deleting: /tmp/null1588913299 +[junitreport] Transform time: 687ms +[junitreport] Deleting: /tmp/null2073971014 junit-integration: [java] @@ -15678,16 +15714,12 @@ [java] Loading package BEAST.app v2.7.6 BEAST.app v2.7.6 BEAST.base v2.7.6 [java] Testing 160 classes [java] Done! - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.base v2.7.6 [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus [java] exception thrown [java] Cannot read the array length because "" is null - [java] - [java] WARNING: Delegated to the 'execute' command. - [java] This behaviour has been deprecated and will be removed in a future release. - [java] Please use the 'execute' command directly. + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.base v2.7.6 [java] [java] [java] @@ -15713,7 +15745,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 1351 ms + [java] Test run finished after 992 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -15727,10 +15759,14 @@ [java] [ 9 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null891588243 + [java] + [java] WARNING: Delegated to the 'execute' command. + [java] This behaviour has been deprecated and will be removed in a future release. + [java] Please use the 'execute' command directly. +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null2004694091 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 300ms -[junitreport] Deleting: /tmp/null891588243 +[junitreport] Transform time: 215ms +[junitreport] Deleting: /tmp/null2004694091 junit-xmlparsertest: [java] @@ -15743,7 +15779,7 @@ [java] │ └─ testClassMap() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 550 ms + [java] Test run finished after 409 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] @@ -15761,15 +15797,15 @@ [java] WARNING: Delegated to the 'execute' command. [java] This behaviour has been deprecated and will be removed in a future release. [java] Please use the 'execute' command directly. -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null248470380 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null761689362 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 170ms -[junitreport] Deleting: /tmp/null248470380 +[junitreport] Transform time: 127ms +[junitreport] Deleting: /tmp/null761689362 junit: BUILD SUCCESSFUL -Total time: 4 minutes 14 seconds +Total time: 3 minutes 25 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -15798,8 +15834,8 @@ dpkg-gencontrol: warning: Depends field of package beast2-mcmc-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'beast2-mcmc' in '../beast2-mcmc_2.7.6+dfsg-1_all.deb'. dpkg-deb: building package 'beast2-mcmc-examples' in '../beast2-mcmc-examples_2.7.6+dfsg-1_all.deb'. +dpkg-deb: building package 'beast2-mcmc' in '../beast2-mcmc_2.7.6+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../beast2-mcmc_2.7.6+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../beast2-mcmc_2.7.6+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -15807,12 +15843,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/96593/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/96593/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/17811 and its subdirectories -I: Current time: Mon Mar 25 14:49:54 -12 2024 -I: pbuilder-time-stamp: 1711421394 +I: removing directory /srv/workspace/pbuilder/96593 and its subdirectories +I: Current time: Mon Apr 28 23:18:08 +14 2025 +I: pbuilder-time-stamp: 1745831888